The generation of high-quality assemblies, even for large eukaryotic genomes, has become a routine task for many biologists thanks to recent advances in sequencing technologies. However, the annotation of these assemblies—a crucial step toward unlocking the biology of the organism of interest—has remained a complex challenge that often requires advanced bioinformatics expertise.


Here, we present MOSGA (Modular Open-Source Genome Annotator), a genome annotation framework for eukaryotic genomes with a user-friendly web-interface that generates and integrates annotations from various tools. The aggregated results can be analyzed with a fully integrated genome browser and are provided in a format ready for submission to NCBI. MOSGA is built on a portable, customizable and easily extendible Snakemake backend, and thus, can be tailored to a wide range of users and projects.

Availability and implementation

We provide MOSGA as a web service at and as a docker container at latest. Source code can be found at

Supplementary information

Supplementary data are available at Bioinformatics online.

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